Partially Saturated Bicyclic Heteroaromatics as an sp3‐Enriched Fragment Collection

Abstract Fragment‐based lead generation has proven to be an effective means of identifying high‐quality lead compounds for drug discovery programs. However, the fragment screening sets often used are principally comprised of sp2‐rich aromatic compounds, which limits the structural (and hence biological) diversity of the library. Herein, we describe strategies for the synthesis of a series of partially saturated bicyclic heteroaromatic scaffolds with enhanced sp3 character. Subsequent derivatization led to a fragment collection featuring regio‐ and stereo‐controlled introduction of substituents on the saturated ring system, often with formation of new stereocenters.

Fragment-based drug discovery (FBDD) is aw ell-established method for generating high-quality hits and leads. [1] Thea pproval of the B-Raf kinase inhibitor vemurafenib (Zelboraf) in 2011 [2] and the Bcl-2 inhibitor venetoclax (Venclexta) in 2016, [3] coupled with the ongoing evaluation of over 20 candidates in clinical trials, [4] validates this approach as acomplementary strategy to other hit-discovery techniques such as high-throughput screening. [5] While the growing prevalence of fragment-based approaches is encouraging,e valuation of many existing fragment libraries shows apredominance of (hetero)aromatic,"flat" compounds,with adeficiencyofc hiral, sp 3 -rich examples. [6,7] Studies by Ritchie et al. [8] and Lovering et al. [9] demonstrate improvements in project progression by,f or example, increasing the fraction of sp 3 centers within molecules or restricting the number of aromatic rings.F urthermore, computational analysis demonstrates that greater 3D conformational character is observed in compounds that have been clinically evaluated in humans,compared to those found in commercial libraries. [10] This indicates the importance of sp 3 -richness in both the design of screening collections and the subsequent development of hits to leads.
Examples of previous studies aiming to synthesize collections of sp 3 -enriched fragments have been limited. Diversityoriented synthesis [7,11] and natural product derivatives [12] have been used to generate 3D fragment collections,b ut there remains an unmet need to access new scaffold types.Recently there have been calls [13] for new approaches and methodologies for designing fragments with multiple synthetically accessible growth vectors in three dimensions,toallow rapid and efficient elaboration of hits to leads after initial screening, with some early success. [14] With these points in mind, the study described herein was aimed at developing efficient synthetic routes to as eries of partially saturated bicyclic heteroaromatic (PSBH) fragments with enhanced sp 3 content relative to existing fragment libraries.C ompounds featuring PSBHs have been shown to display bioactivity against arange of targets (Figure 1), [15] and so as eries of related fragments might be expected to serve effectively as as creening collection for FBDD applications. Thet argets of this study featured av ariable aromatic heterocycle fused to ap artially saturated carbocycle.T he heterocycle could bear either ap olar (e.g., amino) group, which should greatly enhance aqueous solubility,aproperty necessary for fragment screening at higher concentrations, [7,14] or alternatively ahydrophobic (e.g., chloro) group,which can forge key interactions with protein targets. [16] Thes ynthetic route (Scheme 1) employed am odular and divergent approach, using simple cross-coupling and alkylation reactions to install apair of terminal olefins that could be reliably cyclized through ring-closing metathesis (RCM). [17] This allowed excellent control of the carbocycle ring size and the position and orientation of the resultant endocyclic olefin growth vector, which could undergo subsequent functionalization to produce arange of fragments suitable for screening and/or further elaboration.
We selected pyrazole and pyridine as representative aromatic heterocycles.W hilst previous studies have shown the synthesis of related structures, [18] they have incorporated less control over the position of the olefin and do not feature the amino group found in many of our compounds.F urthermore,t here are only very few examples where the olefin is used as ab ranch point and further functionalized beyond simple reduction. [15a,19] Starting from readily available 3-nitro-1H-pyrazole (4), 2-(trimethylsilyl)ethoxymethyl (SEM) protection, selective iodination, and subsequent Suzuki coupling with potassium vinyltrifluoroborate gave vinyl derivative 7a (Table 1). Deprotection followed by N-alkylation with an alkyl bromide of varying C-chain length provided metathesis precursors 9ac,w hich upon treatment with either Grubbs or Hoveyda-Grubbs 2 nd generation catalysts yielded the desired scaffolds 10 a-c.I nclusion of further heteroatoms in the formation of medium-sized partially saturated rings was achieved through treatment of vinyl intermediate 8a with either tosylate 11 (leading, after RCM, to O-containing fragment 10 d), or 3-Boc-1,2,3-oxathiazolidine 2,2-dioxide 12,which gave access to the N-containing scaffold 10 e after allylation and metathesis. Use of ad ifferent Suzuki coupling partner gave methylsubstituted product 7f,w hich could be elaborated to PSBH fragment 10 f.A lternatively,d irect allylation at the C-5 position of SEM-protected intermediate 5 could be achieved upon treatment with lithium diisopropylamide (LDA) and allyl bromide.This led, in an analogous way,toscaffolds 10 gh with non-conjugated olefins.
Asimilar approach was used to generate PSBH scaffolds from pyridine 13 ( Table 2). Attempts to mask the 2-amino group as an itro group proved ineffective since,d espite successful cross-coupling reactions,the 2-nitropyridines were unstable to strong base and did not undergo the desired alkylations at the 4-methyl position. Mono-Boc protection was also unsuitable due to poor yields in the cross-coupling step,p ossibly due to catalyst chelation. The2 -amino group could be rendered synthetically tractable,h owever,e ither through bis-Boc protection or through substitution with a2chloro group,w hich itself can serve as as ynthetic handle. [20] Bis-Boc substrate 14 (prepared in one step from 13)w as functionalized at the 5-position using either Suzuki coupling (for vinyl substituents) or Stille coupling (for allyl substituents) to produce intermediates 15 a,d-f.T reatment with LDA and trapping of the resultant anion with av ariable alkyl bromide electrophile gave ar ange of metathesis substrates (16 a-f), which under standard ring-closing metathesis conditions yielded PSBH scaffolds 17 a-f.T he 2-chloro substrate 18 could be allylated in the 5-position by using an excess of i-PrMgCl·LiCl and trapping the resultant organometallic intermediate with allyl bromide.A llylation at the 4-methyl position and RCM gave scaffold 17 g in superior yields.
Following PSBH synthesis,aseries of simple one-, two-, or three-step functionalizations were performed on selected pyrazole and pyridine scaffolds to demonstrate the synthetic  utility of the olefin p-bond as agrowth vector and to generate av ariety of new stereocenters (Scheme 2). Catalytic hydrogenation of nitropyrazoles 10 a-d,f served to reduce both the olefin p-bond and the nitro group in moderate to good yields,revealing the latent amino functionality and, in the case of 19 f,c reating an ew stereocenter. Other one-step reactions include aziridination, dibromination, allylic oxidation dihydroxylation, difluorocyclopropanation, hydroxybromination, epoxidation, and hydroboration (20-28)t oi ntroduce functionalities at the 4-, 5-and 6positions of the fused pyrazole systems.D emonstrating that these initial products can serve as intermediates to other fragments,the products of hydroboration can react further to incorporate Br, F, and Nsubstituents (30-33), whilst epoxide 26 can be opened by nucleophiles such as fluoride and hydride to form fluorohydrin 35 and alcohol 36.W hilst the yields of some reactions were modest, sufficient material was obtained for full characterization and future screening campaigns.

Angewandte Chemie
Communications formation, both from bromohydrin 43.3 -Chloro fragments 46-51 could also be readily accessed using similar conditions. Calculation of arange of physicochemical properties was carried out on all of the PSBH products.Almost all fragments were shown to conform to the so-called "Rule of Three", aset of criteria commonly associated with greater hit rates in fragment screening collections. [21] Of particular note are the low mean values for molecular weight (190), SlogP (1.45), and "fraction aromatic" (0.43) and the high mean number of chiral centres (0.88), especially when compared to existing commercial libraries (Table 3).
In conclusion, we have developed simple,s calable routes to aseries of partially saturated pyrazole-and pyridine-based scaffolds that can readily undergo ar ange of synthetic transformations to generate acollection of sp 3 -rich fragments, which are suitable for use either as screening members in al ibrary or as intermediates to "higher-content fragments". Thecompounds adhere to recognized guidelines for fragment physicochemical properties,w hilst displaying enhanced sp 3 character and greater chirality,and providing arange of threedimensional growth vectors for synthetic development. It is envisioned that the strategy could be applied to av ast range of analogous scaffolds with varied heterocycles and substituents and that several of the functionalization reactions detailed in Scheme 2c ould be rendered asymmetric based on related precedents. [19,22]